package seqAlignment;

public interface SequenceAligner {

	public void setSequences(String str1, String str2);
	
	public void init();

	public void align();

	public void traceBack();

	public void output();
	
	public void setGapPenaltyFunction(GapPenalty function);
	
	public void setAlignmentScoreFunction(AlignmentScore function);
	
	public String getAlignedStr1();
	
	public String getAlignedStr2();

}